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This distribution is for the bioperl CORBA server applications. You
will need both bioperl and CORBA::ORBit to run this. (available on
CPAN) which itself needs
The overall architecture of this can get quite confusing. Essentially
every biological object is going to have 4 different .pm files associated
with it written by bioperl people and 2 other objects on-the-fly generated
Objects in bioperl:
Bio::xxxxxxI - the interface definition of the object from bioperl's
Bio::xxxxxx - the actual implementation object in pure Perl from bioperl
Objects in bioperl-corba-client
Bio::CorbaClient::xxxxx - A client wrapper that makes a CORBA connection
behave as if it is Bio::xxxxxxI object
Objects in bioperl-corba-server
Bio::CorbaServer::xxxxx - A server wrapper that makes a bioperl object
behave as if it is a BioCorba object
Objects created on-the-fly by CORBA::ORBit
BioCorba::xxxxx - A client proxy object
POA_BioCorba::xxx - A server side server adapator object
The diagram below sketches out what on earth is going on in the case
when we run a perl server which use bioperl-corba-server to provide
objects to a perl client which uses bioperl-corba-client to make
these objects look like "standard" bioperl objects
As the BioCorba IDL is heavily modelled on the bioperl interfaces, it
the wrapper classes are very thin - mainly just delegating the methods
to their respective objects. Having wrapper objects however is a "good thing"
as it provides a cut-out to allow BioCorba and Bioperl not to have to
evolve in lock-step.
The wrapper classes are is also where the memory management rules of
the BioCorba system (a very simple reference counting system) is
implemented. As CORBA is completely agnostic about memory there is a requirement
for these classes to be around to handle this.
| Bio::xxxxI |
| is-a
_______|_________ _____________
|Bio::CorbaClient| has-a | BioCorba:: |
| Client Wrapper |------->| Object | bioperl-corba-client
|________________| |------------|
________________________________ | ______________________________________
CORBA IIOP Connection CORBA::ORBit and ORBit
| bioperl-corba-server
--------------- is-a -------------------
| POA_BioCorba |<------| Bio::CorbaServer|
---------------- | Server Wrapper |
| has-a
| Bio::xxxxI Object |
| is-a
| The real Bio::xxxx |
| Object |
Pretty confusing eh? Once you get used to it, it is fine.
The final point to note is that (of course) it need not be Perl on either
side of the CORBA bridge. Another language could provide these objects
just as easily, or be clients to the bioperl objects. This is how biojava
and biopython can communicate with the bioperl objects cleanly.
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